update median of ratios results type

fslaborg · Jan 25, 2023 · 278bd95 · 278bd95
1 parent e4486b4
commit 278bd95
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Showing 2 changed files with 22 additions and 13 deletions.
diff --git a/src/FSharp.Stats/Signal/Normalization.fs b/src/FSharp.Stats/Signal/Normalization.fs
@@ -18,6 +18,12 @@ module Normalization =
         let std   = Seq.stDev yVal
         yVal |> Vector.map (fun x -> (x - yMean) / std) 
 
+    /// Summary of the median of ratios (mor) normalization with normed data and determined correctionfactors.
+    type MorResult = {
+        CorrFactors : seq<float>
+        NormedData : Matrix<float>
+    } with static member Create cf nd = {CorrFactors=cf;NormedData=nd}
+
     /// As used by Deseq2, see: https://github.com/hbctraining/DGE_workshop/blob/master/lessons/02_DGE_count_normalization.md 
     ///
     /// Rows are genes, columns are samples
@@ -33,11 +39,12 @@ module Normalization =
                 ) 
             |> Matrix.ofRows
             |> Matrix.mapiCols (fun _ v -> Vector.median v)
-        printfn "%A" sampleWiseCorrectionFactors
-        data
-        |> Matrix.mapi (fun r c v ->
-            v / sampleWiseCorrectionFactors.[c]
-        )
+        let normedData = 
+            data
+            |> Matrix.mapi (fun r c v ->
+                v / sampleWiseCorrectionFactors.[c]
+            )
+        MorResult.Create sampleWiseCorrectionFactors normedData
 
     /// As used by Deseq2, see: https://github.com/hbctraining/DGE_workshop/blob/master/lessons/02_DGE_count_normalization.md 
     ///
@@ -60,11 +67,12 @@ module Normalization =
                 ) 
             |> Matrix.ofCols
             |> Matrix.mapiRows (fun _ v -> Seq.median v)
-        printfn "%A" sampleWiseCorrectionFactors
-        data
-        |> Matrix.mapi (fun r c v ->
-            v / sampleWiseCorrectionFactors.[r]
-        )
+        let normedData = 
+            data
+            |> Matrix.mapi (fun r c v ->
+                v / sampleWiseCorrectionFactors.[r]
+            )
+        MorResult.Create sampleWiseCorrectionFactors normedData
 
     /// As used by Deseq2, see: https://github.com/hbctraining/DGE_workshop/blob/master/lessons/02_DGE_count_normalization.md 
     ///

diff --git a/tests/FSharp.Stats.Tests/Signal.fs b/tests/FSharp.Stats.Tests/Signal.fs
@@ -119,13 +119,13 @@ let normalizationTests =
 
             let result = Normalization.medianOfRatios table
 
-            TestExtensions.sequenceEqual 4 result expectedNormalizedTable "Value was not normalized correctly"
+            TestExtensions.sequenceEqual 4 result.NormedData expectedNormalizedTable "Value was not normalized correctly"
 
         testCase "MedianOfRatiosIgnoreNans" <| fun() ->
 
             let result = Normalization.medianOfRatiosBy (fun x -> if System.Double.IsNaN x then 0.1 else x) tableWithNan
 
-            Expect.hasCountOf  result 2u System.Double.IsNaN "Only initial nan values should be nans afterwards"
+            Expect.hasCountOf result.NormedData 2u System.Double.IsNaN "Only initial nan values should be nans afterwards"
 
         testCase "MedianOfRatioWides" <| fun() ->
 
@@ -134,7 +134,8 @@ let normalizationTests =
                 table
                 |> Matrix.transpose
                 |> Normalization.medianOfRatios
+                |> fun x -> x.NormedData
                 |> Matrix.transpose
-            TestExtensions.sequenceEqual 4 result expected "Wide method should return the same result as the non wide method on a transposed matrix"
+            TestExtensions.sequenceEqual 4 result.NormedData expected "Wide method should return the same result as the non wide method on a transposed matrix"
     ]